The Azkals will now have to avoid defeat at home to Tajikistan in next March's final Group F fixture after Tajikistan and Yemen also played out a goalless draw. Thomas Dooley's side remain two points clear at the top of the group and favourites to progress to their first-ever Asian Cup finals.
However, a draw at a country 60 places below them in the FIFA rankings is a major disappointment and ensures a tense wait until they have the chance to clinch their berth in the United Arab Emirates (UAE) in 2019.
The Azkals were the better side throughout, but Nepal battled gamely and occasionally troubled them on the break.
The visitors came close in the 20th minute when Daisuke Sato's cross from the left was headed just wide by Carli de Murga.
Simone Rota headed over from a great position, and Mike Ott missed a fine chance to open the scoring. But the Thailand-based midfielder shot tamely into the keeper's arms.
Just after the hour mark, Rota's long range effort was beaten out, and Phil Younghusband put the rebound wide.
There was an opportunity for the home crowd to bid a fond farewell to Nepal's former Chelsea trialist Anil Gurung, who came on as a substitute in the final 10 minutes for his last international appearance.
But it was the Philippines who came agonisingly close to the opener when Sato's header was cleared off the line in the 84th minute. And there was more drama in added time when de Murga got on the end of Neil Etheridge's free kick but his header came back off the post.
Like the Azkals, Vietnam put on a laboured performance as they drew 0-0 at home to Afghanistan in Group C. But the point was enough to seal qualification as it kept them six points clear of their opponents.
The result may have been disappointing but new head coach Park Hang-seo will be delighted to have clinched their place in the United Arab Emirates before Matchday 6.
Jordan won 1-0 in Cambodia in the Group C's other game to leapfrog Vietnam into top spot and join the Vietnamese in the UAE.
Myanmar stayed firmly in contention to qualify as a 2-2 draw in India kept them within two points of Kyrgyzstan in second place.
Myanmar sensationally took the lead after just 13 seconds through Yan Niang. Sunil Chhetri's 13th-minute penalty drew the hosts level before Kyaw Ko Ko's long-range effort put the visitors back in front.
A fine finish from Jeje Lalpekhula brought India level again in the 69th minute, and Myanmar's rescheduled away fixture in Kyrgyzstan will now be crucial in deciding who comes second in the group behind India.
Kyrgyzstan were given a fright in Macau when they almost blew a three-goal lead. With 20 minutes left, they led 3-0, but Macau pulled two goals back before the two-goal lead was restored in the 84th minute. However, a Carlo Fernandes strike three minutes from time ensured a nervy finale but Kyrgyzstan prevailed 4-3 in the end.
A 1-0 victory by Lebanon over 10-man Hong Kong left the Dragons with a huge mountain to climb if they are to qualify. Hassan Maatouk's 43rd-minute penalty came after Tan Chun Lok was red-carded, and Hong Kong now need an unlikely victory in North Korea next year to progress.
The Koreans' back-to-back 4-1 wins over Malaysia in the last week look to have been decisive in deciding who qualifies alongside Lebanon from Group B.
In Group E, Chinese Taipei suffered a bitter disappointment as a 2-1 defeat in Turkmenistan saw them exit the competition. After last month's rousing home win over Bahrain, hopes had been high. But this defeat, combined with Bahrain's 3-0 win in Singapore, means Chinese Taipei join the Lions in missing out.
There was nothing but pride to play for in Group D, with both qualification spots already settled. Oman won 4-2 in Bhutan, while Palestine thrashed Maldives 8-1.
